Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YY982

Calculation Name: 1EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P47123

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2053997.353731
FMO2-HF: Nuclear repulsion 1980100.649715
FMO2-HF: Total energy -73896.704016
FMO2-MP2: Total energy -74113.854034


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:30:SER)


Summations of interaction energy for fragment #1(A:30:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-16.94-12.1240.33-2.415-2.729-0.004
Interaction energy analysis for fragmet #1(A:30:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.009
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A32ASN0-0.042-0.0333.699-0.1062.631-0.013-1.428-1.2950.006
4A33ASN0-0.007-0.0286.3450.1910.1910.0000.0000.0000.000
5A34LYS10.9300.9619.3481.2511.2510.0000.0000.0000.000
6A35GLU-1-0.895-0.94112.612-0.251-0.2510.0000.0000.0000.000
7A36VAL0-0.051-0.02015.388-0.029-0.0290.0000.0000.0000.000
8A37GLU-1-0.932-0.97218.520-0.201-0.2010.0000.0000.0000.000
9A38LEU0-0.024-0.01820.418-0.026-0.0260.0000.0000.0000.000
10A39TYR0-0.004-0.05223.7200.0270.0270.0000.0000.0000.000
11A40GLY0-0.019-0.01227.4840.0220.0220.0000.0000.0000.000
12A41GLY00.0230.01925.1430.0120.0120.0000.0000.0000.000
13A42ALA0-0.043-0.00826.0360.0170.0170.0000.0000.0000.000
14A43ILE0-0.026-0.01321.9920.0260.0260.0000.0000.0000.000
15A44THR0-0.0020.01719.233-0.017-0.0170.0000.0000.0000.000
16A45THR00.007-0.00316.4570.0010.0010.0000.0000.0000.000
17A46VAL0-0.049-0.02011.045-0.008-0.0080.0000.0000.0000.000
18A47VAL00.0340.02613.4470.0080.0080.0000.0000.0000.000
19A48PRO00.0410.0239.853-0.063-0.0630.0000.0000.0000.000
20A49PRO0-0.038-0.0039.6300.3640.3640.0000.0000.0000.000
21A50GLY00.0590.01912.736-0.170-0.1700.0000.0000.0000.000
22A51PHE00.0030.01912.4780.0770.0770.0000.0000.0000.000
23A52ILE0-0.021-0.01016.6550.0480.0480.0000.0000.0000.000
24A53ASP-1-0.736-0.81220.304-0.422-0.4220.0000.0000.0000.000
25A54ALA0-0.001-0.02022.5890.0240.0240.0000.0000.0000.000
26A55SER00.022-0.00125.0760.0370.0370.0000.0000.0000.000
27A56THR0-0.082-0.05325.4730.0240.0240.0000.0000.0000.000
28A57LEU0-0.092-0.05326.4230.0200.0200.0000.0000.0000.000
29A58ARG10.8230.89329.3600.3410.3410.0000.0000.0000.000
30A59GLU-1-0.920-0.94230.135-0.216-0.2160.0000.0000.0000.000
31A60VAL0-0.019-0.00627.229-0.011-0.0110.0000.0000.0000.000
32A61PRO00.006-0.00629.6110.0130.0130.0000.0000.0000.000
33A62ASP-1-0.883-0.93930.559-0.186-0.1860.0000.0000.0000.000
34A63THR0-0.057-0.03130.289-0.001-0.0010.0000.0000.0000.000
35A64GLN0-0.106-0.06326.636-0.019-0.0190.0000.0000.0000.000
36A65GLU-1-0.786-0.85723.154-0.328-0.3280.0000.0000.0000.000
37A66VAL0-0.026-0.02522.566-0.020-0.0200.0000.0000.0000.000
38A67TYR0-0.007-0.01718.366-0.033-0.0330.0000.0000.0000.000
39A68VAL0-0.026-0.01919.293-0.019-0.0190.0000.0000.0000.000
40A69ASN0-0.063-0.02813.447-0.011-0.0110.0000.0000.0000.000
41A70SER0-0.066-0.04817.0150.1020.1020.0000.0000.0000.000
42A71ARG10.7790.8759.0952.5162.5160.0000.0000.0000.000
43A72ARG10.7810.86616.5970.7740.7740.0000.0000.0000.000
44A73ASP-1-0.876-0.94816.441-0.892-0.8920.0000.0000.0000.000
45A74GLU-1-0.914-0.93816.229-0.746-0.7460.0000.0000.0000.000
46A75GLU-1-0.926-0.95413.939-1.209-1.2090.0000.0000.0000.000
47A76GLU-1-0.916-0.95810.822-1.376-1.3760.0000.0000.0000.000
48A77PHE0-0.064-0.0337.438-0.016-0.0160.0000.0000.0000.000
49A78GLU-1-0.904-0.9543.048-4.321-3.7610.046-0.139-0.467-0.001
50A79ASP-1-0.883-0.9422.738-12.054-10.7100.299-0.842-0.801-0.009
51A80GLY00.0080.0055.1100.4120.498-0.001-0.002-0.0830.000
52A81LEU0-0.071-0.0416.4880.8670.8670.0000.0000.0000.000
53A82ALA0-0.004-0.0099.628-0.066-0.0660.0000.0000.0000.000
54A83THR0-0.001-0.01312.819-0.113-0.1130.0000.0000.0000.000
55A84ASN0-0.016-0.00415.7810.0210.0210.0000.0000.0000.000
56A85GLU-1-0.750-0.84613.204-1.301-1.3010.0000.0000.0000.000
57A86SER0-0.022-0.00916.7470.0220.0220.0000.0000.0000.000
58A87ILE0-0.022-0.01514.4360.0000.0000.0000.0000.0000.000
59A88ILE00.0280.01918.7410.0130.0130.0000.0000.0000.000
60A89VAL0-0.027-0.00820.1570.0050.0050.0000.0000.0000.000
61A90ASP-1-0.752-0.87122.656-0.217-0.2170.0000.0000.0000.000
62A91LEU0-0.065-0.01426.2350.0180.0180.0000.0000.0000.000
63A92LEU00.009-0.00128.5220.0050.0050.0000.0000.0000.000
64A93GLU-1-0.887-0.94230.871-0.083-0.0830.0000.0000.0000.000
65A94THR0-0.097-0.07132.220-0.005-0.0050.0000.0000.0000.000
66A95VAL0-0.015-0.00131.5320.0020.0020.0000.0000.0000.000
67A96ASP-1-0.906-0.94134.099-0.040-0.0400.0000.0000.0000.000
68A97LYS10.7660.86433.2180.0340.0340.0000.0000.0000.000
69A98SER0-0.015-0.02233.432-0.002-0.0020.0000.0000.0000.000
70A99ASP-1-0.851-0.92430.8280.0270.0270.0000.0000.0000.000
71A100LEU0-0.0360.00224.326-0.010-0.0100.0000.0000.0000.000
72A101LYS10.8400.90726.185-0.023-0.0230.0000.0000.0000.000
73A102GLU-1-0.846-0.92727.663-0.034-0.0340.0000.0000.0000.000
74A103ALA0-0.0120.00329.185-0.013-0.0130.0000.0000.0000.000
75A104TRP0-0.022-0.03521.322-0.002-0.0020.0000.0000.0000.000
76A105GLN0-0.032-0.03026.650-0.009-0.0090.0000.0000.0000.000
77A106PHE0-0.0100.00528.378-0.007-0.0070.0000.0000.0000.000
78A107HIS10.8700.90827.2270.1090.1090.0000.0000.0000.000
79A108VAL0-0.015-0.00224.036-0.021-0.0210.0000.0000.0000.000
80A109GLU-1-0.854-0.92126.716-0.136-0.1360.0000.0000.0000.000
81A110ASP-1-0.813-0.90129.843-0.137-0.1370.0000.0000.0000.000
82A111LEU0-0.041-0.02024.034-0.014-0.0140.0000.0000.0000.000
83A112THR0-0.012-0.03026.508-0.013-0.0130.0000.0000.0000.000
84A113GLU-1-0.956-0.97128.744-0.121-0.1210.0000.0000.0000.000
85A114LEU0-0.059-0.01429.3860.0050.0050.0000.0000.0000.000
86A115ASN0-0.076-0.03127.236-0.013-0.0130.0000.0000.0000.000
87A116GLY0-0.051-0.02631.2120.0020.0020.0000.0000.0000.000
88A117THR0-0.019-0.04629.1110.0080.0080.0000.0000.0000.000
89A118THR0-0.059-0.03932.1350.0060.0060.0000.0000.0000.000
90A119LYS10.8640.93630.2130.0940.0940.0000.0000.0000.000
91A120TRP0-0.022-0.02325.233-0.014-0.0140.0000.0000.0000.000
92A121GLU-1-0.919-0.96025.395-0.054-0.0540.0000.0000.0000.000
93A122ALA00.0270.01122.494-0.029-0.0290.0000.0000.0000.000
94A123LEU0-0.046-0.02719.0810.0240.0240.0000.0000.0000.000
95A124GLN0-0.033-0.02214.271-0.008-0.0080.0000.0000.0000.000
96A125GLU-1-0.816-0.89018.851-0.029-0.0290.0000.0000.0000.000
97A126ASP-1-0.813-0.87016.7030.2260.2260.0000.0000.0000.000
98A127THR0-0.0220.00119.740-0.038-0.0380.0000.0000.0000.000
99A128VAL0-0.042-0.02217.0650.0440.0440.0000.0000.0000.000
100A129GLN0-0.022-0.02219.5310.0220.0220.0000.0000.0000.000
101A130GLN00.025-0.00722.688-0.041-0.0410.0000.0000.0000.000
102A131GLY00.0030.00226.198-0.003-0.0030.0000.0000.0000.000
103A132THR00.0020.00324.856-0.011-0.0110.0000.0000.0000.000
104A133LYS10.9250.98218.914-0.024-0.0240.0000.0000.0000.000
105A134PHE00.0160.00621.2000.0460.0460.0000.0000.0000.000
106A135THR00.011-0.00216.365-0.026-0.0260.0000.0000.0000.000
107A136GLY00.0430.01118.2580.0520.0520.0000.0000.0000.000
108A137LEU0-0.054-0.00214.184-0.066-0.0660.0000.0000.0000.000
109A138VAL0-0.001-0.00118.3890.0500.0500.0000.0000.0000.000
110A139MET00.0090.01321.587-0.057-0.0570.0000.0000.0000.000
111A140GLU-1-0.774-0.83523.814-0.166-0.1660.0000.0000.0000.000
112A141VAL0-0.033-0.02927.220-0.001-0.0010.0000.0000.0000.000
113A142ALA0-0.042-0.02129.5810.0100.0100.0000.0000.0000.000
114A143ASN00.0660.02332.0010.0070.0070.0000.0000.0000.000
115A144LYS10.9570.97134.4610.1340.1340.0000.0000.0000.000
116A145TRP0-0.038-0.01133.9950.0110.0110.0000.0000.0000.000
117A146GLY0-0.024-0.00737.5950.0040.0040.0000.0000.0000.000
118A147LYS10.7970.89335.5770.1260.1260.0000.0000.0000.000
119A148PRO00.0610.04131.088-0.010-0.0100.0000.0000.0000.000
120A149ASP-1-0.877-0.92529.178-0.188-0.1880.0000.0000.0000.000
121A150LEU0-0.091-0.04830.9180.0020.0020.0000.0000.0000.000
122A151ALA0-0.041-0.03129.632-0.003-0.0030.0000.0000.0000.000
123A152GLN0-0.049-0.03421.9940.0240.0240.0000.0000.0000.000
124A153THR00.0480.03122.8470.0040.0040.0000.0000.0000.000
125A154VAL00.0030.00021.466-0.045-0.0450.0000.0000.0000.000
126A155VAL0-0.0150.00117.6570.0450.0450.0000.0000.0000.000
127A156ILE00.018-0.00119.267-0.059-0.0590.0000.0000.0000.000
128A157GLY00.0000.00916.4880.0540.0540.0000.0000.0000.000
129A158VAL00.0300.00317.514-0.021-0.0210.0000.0000.0000.000
130A159ALA0-0.026-0.01117.8800.0460.0460.0000.0000.0000.000
131A160LEU0-0.0200.02119.990-0.015-0.0150.0000.0000.0000.000
132A161ILE0-0.025-0.02919.5530.0360.0360.0000.0000.0000.000
133A162ARG10.7850.86323.5950.0310.0310.0000.0000.0000.000
134A163LEU0-0.030-0.00425.1020.0200.0200.0000.0000.0000.000
135A164THR00.024-0.01528.647-0.004-0.0040.0000.0000.0000.000
136A165GLN0-0.077-0.03231.729-0.004-0.0040.0000.0000.0000.000
137A166PHE0-0.011-0.02230.5620.0020.0020.0000.0000.0000.000
138A167ASP-1-0.872-0.88533.409-0.063-0.0630.0000.0000.0000.000
139A168THR00.0240.01228.870-0.012-0.0120.0000.0000.0000.000
140A169ASP-1-0.760-0.83928.228-0.062-0.0620.0000.0000.0000.000
141A170VAL0-0.008-0.01123.177-0.014-0.0140.0000.0000.0000.000
142A171VAL00.009-0.00323.5630.0130.0130.0000.0000.0000.000
143A172ILE0-0.007-0.00117.614-0.023-0.0230.0000.0000.0000.000
144A173SER0-0.011-0.00419.8550.0200.0200.0000.0000.0000.000
145A174ILE00.003-0.00614.064-0.052-0.0520.0000.0000.0000.000
146A175ASN0-0.019-0.01117.7540.0570.0570.0000.0000.0000.000
147A176VAL00.0310.00314.987-0.100-0.1000.0000.0000.0000.000
148A177PRO0-0.0030.00617.7260.0650.0650.0000.0000.0000.000
149A178LEU0-0.0090.00517.288-0.064-0.0640.0000.0000.0000.000
150A179THR00.013-0.00917.5560.0510.0510.0000.0000.0000.000
151A180LYS10.9630.96720.1920.2920.2920.0000.0000.0000.000
152A181GLU-1-0.858-0.92118.819-0.458-0.4580.0000.0000.0000.000
153A182GLU-1-0.712-0.80314.691-0.767-0.7670.0000.0000.0000.000
154A183ALA00.0430.02318.6380.0370.0370.0000.0000.0000.000
155A184SER0-0.115-0.06821.8280.0450.0450.0000.0000.0000.000
156A185GLN0-0.020-0.03316.161-0.045-0.0450.0000.0000.0000.000
157A186ALA00.0670.03620.4720.0420.0420.0000.0000.0000.000
158A187SER0-0.037-0.01221.4580.0280.0280.0000.0000.0000.000
159A188ASN0-0.132-0.07023.2790.0340.0340.0000.0000.0000.000
160A189LYS10.8900.93023.1610.0560.0560.0000.0000.0000.000
161A190GLU-1-0.852-0.88618.582-0.104-0.1040.0000.0000.0000.000
162A191LEU00.0150.00114.099-0.034-0.0340.0000.0000.0000.000
163A192PRO00.0060.00714.7860.0000.0000.0000.0000.0000.000
164A193ALA00.0440.0099.519-0.015-0.0150.0000.0000.0000.000
165A194ARG10.7860.8479.6610.8870.8870.0000.0000.0000.000
166A195CYS0-0.017-0.00410.808-0.073-0.0730.0000.0000.0000.000
167A196HIS0-0.0120.0007.505-0.076-0.0760.0000.0000.0000.000
168A197ALA0-0.011-0.0096.9830.1350.1350.0000.0000.0000.000
169A198VAL00.0430.0147.983-0.087-0.0870.0000.0000.0000.000
170A199TYR0-0.025-0.03210.9520.0560.0560.0000.0000.0000.000
171A200GLN0-0.016-0.0064.2630.8920.981-0.001-0.004-0.0830.000
172A201LEU00.0260.0128.6290.0940.0940.0000.0000.0000.000
173A202LEU0-0.0170.0049.5650.1740.1740.0000.0000.0000.000
174A203GLN0-0.012-0.02211.4040.2020.2020.0000.0000.0000.000
175A204GLU-1-0.876-0.9227.683-0.816-0.8160.0000.0000.0000.000
176A205MET00.0020.01411.3120.0500.0500.0000.0000.0000.000
177A206VAL00.0290.01214.3150.0770.0770.0000.0000.0000.000
178A207ARG10.8430.92810.032-0.236-0.2360.0000.0000.0000.000
179A208LYS10.8460.9009.6400.3690.3690.0000.0000.0000.000
180A209PHE00.0350.04315.389-0.028-0.0280.0000.0000.0000.000
181A210HIS0-0.074-0.04017.9990.0690.0690.0000.0000.0000.000
182A211VAL00.0390.01921.479-0.025-0.0250.0000.0000.0000.000
183A212VAL0-0.052-0.02623.5570.0260.0260.0000.0000.0000.000
184A213ASP-1-0.856-0.91126.092-0.072-0.0720.0000.0000.0000.000
185A214THR0-0.014-0.01929.620-0.009-0.0090.0000.0000.0000.000
186A215SER0-0.134-0.06931.4400.0000.0000.0000.0000.0000.000
187A216LEU00.0000.00828.529-0.003-0.0030.0000.0000.0000.000
188A217PHE0-0.001-0.00628.024-0.003-0.0030.0000.0000.0000.000
189A218ALA0-0.035-0.01433.9730.0120.0120.0000.0000.0000.000